Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Biodiversität im Grünland – unverzichtbar für Landwirtschaft und Gesellschaft: Stellungnahme des Wissenschaftlichen Beirats für Biodiversität
Gerowitt, B. ; Schröder, S. ; Dempfle, L. ; Engels, E.M. ; Engels, J. ; Feindt, P.H. ; Graner, A. ; Hamm, U. ; Heissenhuber, A. ; Schulte-Coerne, H. ; Wolters, V. - \ 2013
Bonn : Bundesanstalt für Landwirtschaft und Ernährung - 20 p.
Association mapping of salt tolerance in barley (Hordeum vulgare L.)
Nguyen Viet Long, L. ; Dolstra, O. ; Malosetti, M. ; Kilian, B. ; Graner, A. ; Visser, R.G.F. ; Linden, C.G. van der - \ 2013
Theoretical and Applied Genetics 126 (2013)9. - ISSN 0040-5752 - p. 2335 - 2351.
genome-wide association - abiotic stress tolerance - quantitative trait loci - linkage disequilibrium - population-structure - salinity stress - expression analysis - ion homeostasis - wild barley - molecular markers
A spring barley collection of 192 genotypes from a wide geographical range was used to identify quantitative trait loci (QTLs) for salt tolerance traits by means of an association mapping approach using a thousand SNP marker set. Linkage disequilibrium (LD) decay was found with marker distances spanning 2–8 cM depending on the methods used to account for population structure and genetic relatedness between genotypes. The association panel showed large variation for traits that were highly heritable under salt stress, including biomass production, chlorophyll content, plant height, tiller number, leaf senescence and shoot Na+, shoot Cl- and shoot, root Na+/K+ contents. The significant correlations between these traits and salt tolerance (defined as the biomass produced under salt stress relative to the biomass produced under control conditions) indicate that these traits contribute to (components of) salt tolerance. Association mapping was performed using several methods to account for population structure and minimize false-positive associations. This resulted in the identification of a number of genomic regions that strongly influenced salt tolerance and ion homeostasis, with a major QTL controlling salt tolerance on chromosome 6H, and a strong QTL for ion contents on chromosome 4H.
Genome-wide association studies for Agronomical Traits in a world wide Spring Barley Collection
Pasam, R.K. ; Sharma, R. ; Malosetti, M. ; Eeuwijk, F.A. van; Haseneyer, G. ; Kilian, B. ; Graner, A. - \ 2012
BMC Plant Biology 12 (2012). - ISSN 1471-2229
multilocus genotype data - hordeum-vulgare l. - linkage disequilibrium - population-structure - complex traits - flowering time - qtl analysis - missing heritability - haplotype structure - genetic diversity
Background Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS. Results Population structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions. Conclusions Our results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity
Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.)
Varshney, R.K. ; Paulo, M.J. ; Grando, S. ; Eeuwijk, F.A. van; Keizer, L.C.P. ; Guo, P. ; Ceccarelli, S. ; Kilian, A. ; Baum, M. ; Graner, A. - \ 2012
Field Crops Research 126 (2012). - ISSN 0378-4290 - p. 171 - 180.
multilocus genotype data - triticum-aestivum l. - ab-qtl analysis - linkage disequilibrium - population-structure - agronomic traits - spring barley - mapping population - allele frequencies - yield components
Genome wide association (GWA) analysis of yield, yield components, developmental, physiological and anatomical traits was conducted for a barley germplasm collection consisting of 185 cultivated (Hordeum vulgare L.) and 38 wild (Hordeum spontaneum L.) genotypes, originating from 30 countries of four continents. Phenotypic evaluations were performed at a dry (Breda) and wet (Tel Hadya) location in Syria. Genome wide association study was done with 816 markers comprised of 710 diversity array technology (DArT), 61 single nucleotide polymorphism (SNP) and 45 microsatellite or simple sequence repeat (SSR) markers. Diversity analysis revealed 5 groups of germplasm, related to origin (Middle East, North Africa), structural information (two-rows), and domestication (wild versus domesticated). Linkage disequilibrium (LD) decayed after 3 cM with a few exceptions at 10 and 15 cM. Although a few QTLs were identified that differed between the dry and wet site, these QTLs explained low phenotypic variation and could not unequivocally be related to drought tolerance when compared to earlier linkage mapping based QTL analysis studies. Therefore, GWA analysis seems to be not very effective for identification of major QTLs for complex traits like drought tolerance in highly structured germplasm collections
A high density barley microsatellite consensus map with 775 SSR loci
Varshney, R.K. ; Marcel, T.C. ; Ramsay, L. ; Russell, J. ; Roder, M.S. ; Stein, N. ; Waugh, R. ; Langridge, P. ; Niks, R.E. ; Graner, A. - \ 2007
Theoretical and Applied Genetics 114 (2007)6. - ISSN 0040-5752 - p. 1091 - 1103.
simple sequence repeats - genetic-linkage maps - hordeum-vulgare l. - abiotic stress - aflp markers - bread wheat - genome - diversity - plants - rflp
A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWBDom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMapA (R) 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.
A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues
Marcel, T.C. ; Varshney, R.K. ; Barbieri, M. ; Jafary, H. ; Kock, M.J.D. de; Graner, A. ; Niks, R.E. - \ 2007
Theoretical and Applied Genetics 114 (2007)3. - ISSN 0040-5752 - p. 487 - 500.
powdery mildew resistance - quantitative trait loci - aflp markers - microsatellite markers - disease-resistance - ssr-markers - linkage map - genome - rice - cloning
A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP markers. Another set of 61 genic microsatellites was mapped for the first time using a newly developed fluorescent labelling strategy, referred to as A/T labelling. The final map contains 3,258 markers spanning 1,081 centiMorgans (cM) with an average distance between two adjacent loci of 0.33 cM. This is the highest density of markers reported for a barley genetic map to date. The consensus map was divided into 210 BINs of about 5 cM each in which were placed 19 quantitative trait loci (QTL) contributing to the partial resistance to barley leaf rust (Puccinia hordei Otth) in five of the integrated populations. Each parental barley combination segregated for different sets of QTLs, with only few QTLs shared by any pair of cultivars. Defence gene homologues (DGH) were identified by tBlastx homology to known genes involved in the defence of plants against microbial pathogens. Sixty-three DGHs were located into the 210 BINs in order to identify candidate genes responsible for the QTL effects. Eight BINs were co-occupied by a QTL and DGH(s). The positional candidates identified are receptor-like kinase, WIR1 homologues and several defence response genes like peroxidases, superoxide dismutase and thaumatin
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